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- PDB-8dyo: Cryo-EM structure of Importin-4 bound to RanGTP -

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Basic information

Entry
Database: PDB / ID: 8dyo
TitleCryo-EM structure of Importin-4 bound to RanGTP
Components
  • GTP-binding nuclear protein GSP1/CNR1
  • Importin-4
KeywordsPROTEIN TRANSPORT / Importin / Karyopherin / GTPase / nuclear import
Function / homology
Function and homology information


regulation of cell cycle phase transition / Postmitotic nuclear pore complex (NPC) reformation / regulation of nucleocytoplasmic transport / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear localization sequence binding / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus / nucleus organization / protein localization to nucleus / ribosomal subunit export from nucleus ...regulation of cell cycle phase transition / Postmitotic nuclear pore complex (NPC) reformation / regulation of nucleocytoplasmic transport / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear localization sequence binding / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus / nucleus organization / protein localization to nucleus / ribosomal subunit export from nucleus / small GTPase binding / protein import into nucleus / GTPase activity / chromatin / GTP binding / protein-containing complex / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Importin beta family / TOG domain / TOG / HEAT-like repeat / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain ...Importin beta family / TOG domain / TOG / HEAT-like repeat / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTP-binding nuclear protein GSP1/CNR1 / Importin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsBernardes, N.E. / Fung, H.Y.J. / Li, Y. / Chen, Z. / Chook, Y.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141461 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069909 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP170644 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structure of IMPORTIN-4 bound to the H3-H4-ASF1 histone-histone chaperone complex.
Authors: Natália Elisa Bernardes / Ho Yee Joyce Fung / Yang Li / Zhe Chen / Yuh Min Chook /
Abstract: IMPORTIN-4, the primary nuclear import receptor of core histones H3 and H4, binds the H3-H4 dimer and histone chaperone ASF1 prior to nuclear import. However, how H3-H3-ASF1 is recognized for ...IMPORTIN-4, the primary nuclear import receptor of core histones H3 and H4, binds the H3-H4 dimer and histone chaperone ASF1 prior to nuclear import. However, how H3-H3-ASF1 is recognized for transport cannot be explained by available crystal structures of IMPORTIN-4-histone tail peptide complexes. Our 3.5-Å IMPORTIN-4-H3-H4-ASF1 cryoelectron microscopy structure reveals the full nuclear import complex and shows a binding mode different from suggested by previous structures. The N-terminal half of IMPORTIN-4 clamps the globular H3-H4 domain and H3 αN helix, while its C-terminal half binds the H3 N-terminal tail weakly; tail contribution to binding energy is negligible. ASF1 binds H3-H4 without contacting IMPORTIN-4. Together, ASF1 and IMPORTIN-4 shield nucleosomal H3-H4 surfaces to chaperone and import it into the nucleus where RanGTP binds IMPORTIN-4, causing large conformational changes to release H3-H4-ASF1. This work explains how full-length H3-H4 binds IMPORTIN-4 in the cytoplasm and how it is released in the nucleus.
History
DepositionAug 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Importin-4
B: GTP-binding nuclear protein GSP1/CNR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,2054
Polymers143,6572
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Importin-4 / Imp4 / Importin-4b / Imp4b / Ran-binding protein 4 / RanBP4


Mass: 118832.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IPO4, IMP4B, RANBP4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TEX9
#2: Protein GTP-binding nuclear protein GSP1/CNR1 / Chromosome stability protein 17 / GTPase Ran homolog / Genetic suppressor of PRP20-1


Mass: 24825.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Truncated yeast Ran (residues 1-179) with the Q71L mutation
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GSP1, CNR1, CST17, YLR293C, L8003.19 / Production host: Escherichia coli (E. coli) / References: UniProt: P32835
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of Importin-4 bound to RanGTP / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1400 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
EM software
IDNameVersionCategory
10cryoSPARC3.3.1initial Euler assignment
11cryoSPARC3.3.1final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16089 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039389
ELECTRON MICROSCOPYf_angle_d0.84712760
ELECTRON MICROSCOPYf_dihedral_angle_d4.8561283
ELECTRON MICROSCOPYf_chiral_restr0.0491501
ELECTRON MICROSCOPYf_plane_restr0.0061647

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